[med-svn] [nanopolish] 03/08: Refresh and update patches

Afif Elghraoui afif at moszumanska.debian.org
Fri Aug 12 07:08:42 UTC 2016 

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afif pushed a commit to branch master
in repository nanopolish.

commit 364b82db6ab13f6a4dba56d7dd005530b4e686ad
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Aug 11 20:31:39 2016 -0700

    Refresh and update patches
---
 debian/patches/adjust-include-path.patch | 136 ++-----------------------------
 debian/patches/compiler-flags.patch      |  17 ++--
 debian/patches/fix-ftbfs-with-gcc6.patch |   6 +-
 debian/patches/reproducible.patch        |   6 +-
 4 files changed, 21 insertions(+), 144 deletions(-)

diff --git a/debian/patches/adjust-include-path.patch b/debian/patches/adjust-include-path.patch
index 8ad2e35..ad8836b 100644
--- a/debian/patches/adjust-include-path.patch
+++ b/debian/patches/adjust-include-path.patch
@@ -1,9 +1,9 @@
 Description: Adjust #include statements
  Use angle brackets rather than quotes so that the library headers can be
  pulled in from prespecified locations.
-Author: Afif Elghraoui <afif at ghraoui.name>
+Author: Afif Elghraoui <afif at debian.org>
 Forwarded: https://github.com/jts/nanopolish/pull/33
-Last-Update: 2016-01-18
+Last-Update: 2016-08-11
 --- nanopolish.orig/src/nanopolish_poremodel.cpp
 +++ nanopolish/src/nanopolish_poremodel.cpp
 @@ -11,7 +11,7 @@
@@ -17,10 +17,10 @@ Last-Update: 2016-01-18
  {
 --- nanopolish.orig/src/nanopolish_poremodel.h
 +++ nanopolish/src/nanopolish_poremodel.h
-@@ -13,7 +13,7 @@
- #include "nanopolish_common.h"
- #include <inttypes.h>
+@@ -15,7 +15,7 @@
  #include <string>
+ #include <map>
+ #include "nanopolish_model_names.h"
 -#include "../fast5/src/fast5.hpp"
 +#include <fast5.hpp>
  
@@ -28,130 +28,12 @@ Last-Update: 2016-01-18
  struct PoreModelStateParams
 --- nanopolish.orig/src/nanopolish_squiggle_read.cpp
 +++ nanopolish/src/nanopolish_squiggle_read.cpp
-@@ -9,7 +9,7 @@
- #include <algorithm>
- #include "nanopolish_common.h"
+@@ -11,7 +11,7 @@
  #include "nanopolish_squiggle_read.h"
+ #include "nanopolish_pore_model_set.h"
+ #include "nanopolish_methyltrain.h"
 -#include "src/fast5.hpp"
 +#include <fast5.hpp>
  
  //
- SquiggleRead::SquiggleRead(const std::string& name, const std::string& path) :
---- nanopolish.orig/src/alignment/nanopolish_alignment_db.cpp
-+++ nanopolish/src/alignment/nanopolish_alignment_db.cpp
-@@ -9,9 +9,9 @@
- #include <assert.h>
- #include <algorithm>
- #include "nanopolish_alignment_db.h"
--#include "htslib/faidx.h"
--#include "htslib/hts.h"
--#include "htslib/sam.h"
-+#include <htslib/faidx.h>
-+#include <htslib/hts.h>
-+#include <htslib/sam.h>
- 
- // Various file handle and structures
- // needed to traverse a bam file
---- nanopolish.orig/src/alignment/nanopolish_anchor.cpp
-+++ nanopolish/src/alignment/nanopolish_anchor.cpp
-@@ -10,7 +10,7 @@
- #include <string>
- #include <stdio.h>
- #include <assert.h>
--#include "htslib/faidx.h"
-+#include <htslib/faidx.h>
- #include "nanopolish_common.h"
- #include "nanopolish_anchor.h"
- #include "nanopolish_squiggle_read.h"
---- nanopolish.orig/src/alignment/nanopolish_anchor.h
-+++ nanopolish/src/alignment/nanopolish_anchor.h
-@@ -10,8 +10,8 @@
- #define NANOPOLISH_ANCHOR_H
- 
- #include <memory>
--#include "htslib/hts.h"
--#include "htslib/sam.h"
-+#include <htslib/hts.h>
-+#include <htslib/sam.h>
- #include "nanopolish_common.h"
- #include "nanopolish_squiggle_read.h"
- #include "nanopolish_fast5_map.h"
---- nanopolish.orig/src/alignment/nanopolish_eventalign.cpp
-+++ nanopolish/src/alignment/nanopolish_eventalign.cpp
-@@ -19,7 +19,7 @@
- #include <set>
- #include <omp.h>
- #include <getopt.h>
--#include "htslib/faidx.h"
-+#include <htslib/faidx.h>
- #include "nanopolish_eventalign.h"
- #include "nanopolish_iupac.h"
- #include "nanopolish_poremodel.h"
---- nanopolish.orig/src/alignment/nanopolish_eventalign.h
-+++ nanopolish/src/alignment/nanopolish_eventalign.h
-@@ -9,8 +9,8 @@
- #ifndef NANOPOLISH_EVENTALIGN_H
- #define NANOPOLISH_EVENTALIGN_H
- 
--#include "htslib/faidx.h"
--#include "htslib/sam.h"
-+#include <htslib/faidx.h>
-+#include <htslib/sam.h>
- #include "nanopolish_alphabet.h"
- #include "nanopolish_common.h"
- 
---- nanopolish.orig/src/common/nanopolish_fast5_map.cpp
-+++ nanopolish/src/common/nanopolish_fast5_map.cpp
-@@ -14,7 +14,7 @@
- #include <sys/stat.h>
- #include "nanopolish_fast5_map.h"
- #include "nanopolish_common.h"
--#include "htslib/kseq.h"
-+#include <htslib/kseq.h>
- 
- //
- #define FOFN_SUFFIX ".fast5.fofn"
---- nanopolish.orig/src/nanopolish_call_variants.cpp
-+++ nanopolish/src/nanopolish_call_variants.cpp
-@@ -21,7 +21,7 @@
- #include <set>
- #include <omp.h>
- #include <getopt.h>
--#include "htslib/faidx.h"
-+#include <htslib/faidx.h>
- #include "nanopolish_poremodel.h"
- #include "nanopolish_transition_parameters.h"
- #include "nanopolish_matrix.h"
---- nanopolish.orig/src/nanopolish_getmodel.cpp
-+++ nanopolish/src/nanopolish_getmodel.cpp
-@@ -20,7 +20,7 @@
- #include <set>
- #include <omp.h>
- #include <getopt.h>
--#include "htslib/faidx.h"
-+#include <htslib/faidx.h>
- #include "nanopolish_poremodel.h"
- #include "nanopolish_squiggle_read.h"
- #include "profiler.h"
---- nanopolish.orig/src/nanopolish_methyltest.cpp
-+++ nanopolish/src/nanopolish_methyltest.cpp
-@@ -20,7 +20,7 @@
- #include <set>
- #include <omp.h>
- #include <getopt.h>
--#include "htslib/faidx.h"
-+#include <htslib/faidx.h>
- #include "nanopolish_eventalign.h"
- #include "nanopolish_iupac.h"
- #include "nanopolish_poremodel.h"
---- nanopolish.orig/src/nanopolish_methyltrain.cpp
-+++ nanopolish/src/nanopolish_methyltrain.cpp
-@@ -20,7 +20,7 @@
- #include <set>
- #include <omp.h>
- #include <getopt.h>
--#include "htslib/faidx.h"
-+#include <htslib/faidx.h>
- #include "nanopolish_methyltrain.h"
- #include "nanopolish_eventalign.h"
- #include "nanopolish_iupac.h"
+ SquiggleRead::SquiggleRead(const std::string& name, const std::string& path, const uint32_t flags) :
diff --git a/debian/patches/compiler-flags.patch b/debian/patches/compiler-flags.patch
index dad91eb..6e32878 100644
--- a/debian/patches/compiler-flags.patch
+++ b/debian/patches/compiler-flags.patch
@@ -1,9 +1,9 @@
 Description: Allow adding settings to standard compiler flags
  * Use += for CFLAGS/CXXFLAGS
  * Use LDFLAGS
-Author: Afif Elghraoui <afif at ghraoui.name>
+Author: Afif Elghraoui <afif at debian.org>
 Forwarded: no
-Last-Update: 2016-01-18
+Last-Update: 2016-08-11
 --- nanopolish.orig/Makefile
 +++ nanopolish/Makefile
 @@ -9,9 +9,9 @@
@@ -18,22 +18,17 @@ Last-Update: 2016-01-18
  CXX=g++
  CC=gcc
  HDF5=install
-@@ -95,15 +95,15 @@
- 	$(CXX) -o $@ -c $(CXXFLAGS) $(CPPFLAGS) -fPIC $<
- 
- .c.o:
--	$(CC) -o $@ -c $(CFLAGS) -fPIC $<
-+	$(CC) -o $@ -c $(CFLAGS) $(CPPFLAGS) -fPIC $<
+@@ -108,11 +108,11 @@
  
  # Link main executable
- $(PROGRAM): src/main/nanopolish.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB)
+ $(PROGRAM): src/main/nanopolish.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(EIGEN)
 -	$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS)
-+	$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(LDFLAGS) $(HTS_LIB) $(H5_LIB) $(LIBS)
++	$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS)
  
  # Link test executable
  $(TEST_PROGRAM): src/test/nanopolish_test.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB)
 -	$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS)
-+	$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(LDFLAGS) $(HTS_LIB) $(H5_LIB) $(LIBS)
++	$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS)
  
  test: $(TEST_PROGRAM)
  	./$(TEST_PROGRAM)
diff --git a/debian/patches/fix-ftbfs-with-gcc6.patch b/debian/patches/fix-ftbfs-with-gcc6.patch
index 950f620..534261f 100644
--- a/debian/patches/fix-ftbfs-with-gcc6.patch
+++ b/debian/patches/fix-ftbfs-with-gcc6.patch
@@ -1,8 +1,8 @@
 Description: fix build with GCC6
 Author: Sascha Steinbiss <satta at debian.org>
---- a/src/common/nanopolish_variant.cpp
-+++ b/src/common/nanopolish_variant.cpp
-@@ -24,7 +24,8 @@
+--- nanopolish.orig/src/common/nanopolish_variant.cpp
++++ nanopolish/src/common/nanopolish_variant.cpp
+@@ -29,7 +29,8 @@
                                        const std::string& haplotype)
  {
      AlnParam par = aln_param_nt2nt;
diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch
index 91abfc3..a457fa7 100644
--- a/debian/patches/reproducible.patch
+++ b/debian/patches/reproducible.patch
@@ -2,9 +2,9 @@ Description: make build reproducible
  This patch enforces stable input file ordering w.r.t. source file gathering
  via Make's 'wildcard' directive.
 Author: Sascha Steinbiss <satta at debian.org>
---- a/Makefile
-+++ b/Makefile
-@@ -69,8 +69,8 @@
+--- nanopolish.orig/Makefile
++++ nanopolish/Makefile
+@@ -78,8 +78,8 @@
  #
  
  # Find the source files by searching subdirectories

-- 
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